Electrochemical detection is attractive because it provides high sensitivity, small dimensions, low cost, fast response, and compatibility with microfabrication technologies. (See, e.g., Hughes et al., Science, 254: 74-80 (1991); Mir et al., Electrophoresis, 30: 3386-3397 (2009); Trojanowicz, Anal. Chim. Acta, 653: 36-58 (2009); and, Xu et al., Talanta, 80: 8-18 (2009).) These characteristics have led to the development of a variety of sensors based on amperometric, potentiometric or impedimetric signals and their assembly into arrays for chemical, biochemical and cellular applications. (See, e.g., Yeow et al., Sensors and Actuators B 44: 434-440 (1997); Martinoia et al., Biosensors & Bioelectronics, 16: 1043-1050 (2001); Hammond et al., IEEE Sensors J., 4: 706-712 (2004); Milgrew et al., Sensors and Actuators B 103: 37-42 (2004); Milgrew et al., Sensors and Actuators B, 111-112: 347-353 (2005); Hizawa et al., Sensors and Actuators B, 117: 509-515 (2006); Heer et al., Biosensors and Bioelectronics, 22: 2546-2553 (2007); Barbaro et al., Sensors and Actuators B, 118: 41-46 (2006); Anderson et al., Sensors and Actuators B, 129: 79-86 (2008); Rothberg et al., U.S. patent publication 2009/0127589; and, Rothberg et al., U.K. patent application GB24611127.) Typically in such systems, analytes are randomly distributed among an array of confinement regions, such as microwells (also referred to herein as “wells”) or reaction chambers, and reagents are delivered to such regions by a fluidics system that directs flows of reagents through a flow cell containing the sensor array. Microwells in which reactions take place, as well as empty wells where no reactions take place, may be monitored by one or more electronic sensors associated with each of the microwells.
In one type of electrochemical detection, the fundamental reaction product, or “signal”, is a pH change. The pH change is detected by measuring a change in the surface charge at the bottom of the well. The surface at the bottom of the well buffers the pH change produced as a result of the biological reaction. The resulting change in surface charge due to the biological reaction is sensed by capacitive coupling of the bottom of the well to a floating gate of a chemically-sensitive field effect transistor (chemFET) below the surface. However, the sidewalls of the well are too far removed from the chemFET to contribute to the chemFET signal. Unfortunately, in current implementations, the sidewalls of the well buffer as well as surface at the bottom of the well. For example, FIG. 2A shows a prior art microwell structure with native metal oxide, nitride, or oxinitride surface on both the bottom and sidewall. Hence the sidewall's buffering reduces the signal detected at the bottom of the well.
In view of the above, it would be advantageous to have available a microwell structure and a method of conformal coating and selective etching of microwell sidewalls that reduce sidewall buffering, which overcome the deficiencies of current approaches.